[gmx-developers] Geometry-dependent (non-spherically symmetric) potentials

[ms]

On 11/01/11 16:55, hess at sbc.su.se wrote:
>> On 11/01/11 16:32, hess at sbc.su.se wrote:
>>> Hi,
>>>
>>> Are these 3 particles completely independent or are two of the particles
>>> somehow bound together?
>>> In the latter case you could use and modify the generic charge group
>>> inner loops.
>>
>> Latter case. Thanks for the suggestion -can you elaborate on this, just
>> to help me understanding why and how this is a viable opportunity? :)
>> thanks!
>>
>> m.
>>
>
> Atoms in the same charge group are kept sequential in all circumstances
> in Gromacs, in particular they end up sequentially in the neighbor list.
>
> When you set the env.var. GMX_NBLISTCG interaction are calculated
> charge group wise with plain C code in src/gmxlib/nonbonded/nb_generic_cg.c.
> So you will then have access to all 3 coordinates at once.

Cool! Thanks!
m.

> Berk
>
>>> Berk
>>>
>>>> Hi,
>>>>
>>>> While I understand that all non-bonded gmx potential shapes are
>>>> intended
>>>> to be spherically symmetric, for a project of mine it would be helpful
>>>> to be able to have a non-bonded pair potential which is
>>>> geometry-dependent (that is, depending on the angle between 3 atoms).
>>>>
>>>> Has anything -official or unofficial- of this kind ever been attempted
>>>> on Gromacs and, if yes, are there code examples to look at?
>>>>
>>>> Any kind of advice is welcome!
>>>>
>>>> thanks,
>>>> Massimo
>>>>
>>>> --
>>>> Massimo Sandal, Ph.D.
>>>> http://devicerandom.org
>>>> --
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>>>
>>
>>
>> --
>> Massimo Sandal, Ph.D.
>> http://devicerandom.org
>> --
>> gmx-developers mailing list
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>>
>


-- 
Massimo Sandal, Ph.D.
http://devicerandom.org